Preheat the oven to 375°F (190°C).
Cook the penne pasta in a large pot of salted boiling water according to package instructions until al dente. Drain and set aside.
Heat olive oil in a large skillet over medium heat. Add the chopped onion and cook for 3-4 minutes until softened.
Add the minced garlic and cook for 1 minute until fragrant.
Add the ground turkey to the skillet. Cook, breaking it up with a spoon, until fully cooked and no longer pink, about 6-8 minutes.
Stir in the marinara sauce, dried Italian seasoning, salt, black pepper, and crushed red pepper flakes. Simmer for 5 minutes, stirring occasionally.
In a large mixing bowl, combine the cooked pasta and the turkey sauce mixture. Stir until well combined.
Transfer half of the pasta mixture into a 9×13-inch baking dish. Sprinkle half of the shredded mozzarella and half of the grated Parmesan cheese over the pasta.
Add the remaining pasta mixture on top and then sprinkle the remaining mozzarella and Parmesan cheeses evenly over the casserole.
Bake uncovered in the preheated oven for 20 minutes, or until the cheese is melted and bubbly with a light golden color.
Remove from the oven and let it rest for 5 minutes before serving.
Garnish with chopped fresh parsley and serve warm.